Modeling individual effects in the Cormack-Jolly-Seber model: a state-space formulation

Summary .   In population and evolutionary biology, there exists considerable interest in individual heterogeneity in parameters of demographic models for open populations. However, flexible and practical solutions to the development of such models have proven to be elusive. In this article, I provide a state-space formulation of open population capture–recapture models with individual effects. The state-space formulation provides a generic and flexible framework for modeling and inference in models with individual effects, and it yields a practical means of estimation in these complex problems via contemporary methods of Markov chain Monte Carlo. A straightforward implementation can be achieved in the software package WinBUGS . I provide an analysis of a simple model with constant parameter detection and survival probability parameters. A second example is based on data from a 7-year study of European dippers, in which a model with year and individual effects is fitted.     

Characteristics of Sasa nipponica grassland as a summer forage resource for sika deer on Mt Ohdaigahara, central Japan

Recently, the sika deer, Cervus nippon Temminck, population has increased on Mt Ohdaigahara, central Japan. The dwarf bamboo, Sasa nipponica Makino et Shibata, is a primary forage plant for sika deer in this area. To demonstrate the characteristics of S. nipponica grassland, especially as summer forage for sika deer, the habitat use intensity of sika deer was estimated by fecal densities, and biomass, growth rate, removal by deer and crude protein content were examined. Sika deer utilized the S.nipponica grassland on Mt Ohdaigahara during summer when the biomass, growth rate and crude protein content of S. nipponica were high. The recent increase in the deer population seems to be partly due to S.nipponica grassland being a favorable summer habitat.     

Summer forage biomass and the importance of litterfall for a high-density sika deer population

The biomass of summer forage and their contributions were surveyed to show that litterfall supported a high-density population of sika deer (Cervus nippon Temminck) in summer on Nakanoshima Island, Toya Lake, Japan. In July 1974, the grassland had the highest productivity among understory vegetations (228±55kgha^–1: mean±SE). In deciduous forests, palatable plants occupied only 0.1% of the biomass of 0.872±0.366kgha^–1, and deciduous leaves within the reach of deer (=220cm at height) produced 0.208±0.070kgha^–1. However, litterfall during this period had the highest productivity, 28.7± 5.3kgha^–1. The deer consumed litterfall (75.6% in dry weight), short grasses (17.2%), deciduous forest understory (4.1%), deciduous leaves within the reach of deer (3.0%) and conifer plantation under story (0.1%). It is suggested that the high-density deer population would be maintained by litterfall through the year instead of browsing in deciduous forests, which has been overlooked.     

Degradation of Abies veitchii wave-regeneration on Mt. Misen in Ohmine Mountains: effects of sika deer population

How has the degradation of Abies veitchii wave-regeneration occurred under the sika deer (Cervus nippon) pressure? We conducted tree census and ground vegetation survey in a 1 ha plot in Mt. Misen (Nara prefecture, Japan). We found 15 tree species (over 50 cm in height). Abies accounted for 60.0 % of all living trees, and 46.9 % of Abies were damaged (herbivory, bark stripping and/or fraying) by deer. Spatial distribution of Abies trees showed Abies-wave, although there were few saplings in the dieback zone. Estimated deer population density in 2009 was 57.3 head/km². Number of living Abies and standing dead conifer trees, and ground vegetation cover for each quadrat (5 × 5 m) were used to assign the quadrats into 6 clusters. The hierarchical clustering-approach revealed that living Abies distributed mainly on the moss and/or Carex fernaldiana dominated quadrats, but did not on the Dennstaedtia scabra, or Brachypodium sylvaticum dominated quadrats. While standing dead conifer trees distributed mainly on the Carex dominated quadrats, they hardly occur on the moss, the Dennstaedtia or the Brachypodium dominated quadrats. Regeneration of Abies tree and thus the wave-regeneration is hindered for now owing to deer herbivory and bark-stripping. The ground vegetation under the dieback zone has changed from the moss and/or the Carex dominated one to the Carex, the Dennstaedtia or the Brachypodium covered vegetation with the canopy remained open and without Abies regeneration.     

Bayesian inference for dynamic transcriptional regulation; the Hes1 system as a case study

MOTIVATION: In this study, we address the problem of estimating the parameters of regulatory networks and provide the first application of Markov chain Monte Carlo (MCMC) methods to experimental data. As a case study, we consider a stochastic model of the Hes1 system expressed in terms of stochastic differential equations (SDEs) to which rigorous likelihood methods of inference can be applied. When fitting continuous-time stochastic models to discretely observed time series the lengths of the sampling intervals are important, and much of our study addresses the problem when the data are sparse. RESULTS: We estimate the parameters of an autoregulatory network providing results both for simulated and real experimental data from the Hes1 system. We develop an estimation algorithm using MCMC techniques which are flexible enough to allow for the imputation of latent data on a finer time scale and the presence of prior information about parameters which may be informed from other experiments as well as additional measurement error.     

The effects of population density changes on ecosystem services value: A case study in Western Jilin,China

In recent decades, the semi-arid ecosystem of China's Western Jilin province has changed dramatically due to intensive human activities. This article simulated the population density in Western Jilin using a Kernel Density Estimation method and explored the influence of population density on both the value and structure of ecosystem services in various regions. The results showed that lower population density correlated with higher values of ecosystem services per unit area. Apart from food production value, the value of each type of ecosystem service per unit area decreased as population density increased, with the greatest change observed in the value of waste disposal and the lowest in the value of raw materials. Analysis of demographic change on the structure of ecosystem services value produced a Gourd Phenomenon. Sensitivity analysis showed that the sensitivity coefficient of farmland ecosystems was highest, followed by wetland ecosystems and water ecosystems. Therefore, we should restore farmland to grassland and wetland (with its associated rivers and lakes) when reconstructing the eco-environment in Western Jilin.     

Modeling density dependence in heterogeneous landscapes: Dispersal as a case study

Population models often pose density-dependent rates as relations between current population size on a habitat patch, n, and some threshold size defined by limiting resources, r. In fourteen recent modeling studies incorporating density-dependent dispersal, formulations of the density-dependent rate (or probability) fall into two distinct groups, expressing the rate as a function of n-r or n/r. These two depictions of the same process differ fundamentally: they can cause strikingly different dynamics in otherwise identical systems and they have different scaling properties in heterogeneous landscapes. Here I consider the implications of the two formulations under two broad ecological scenarios: scramble competition for an equally divided resource (e.g. food) and contest competition for an unequally divided resource (e.g. nest sites). In both cases, simple arguments show that the n/r form is preferable when density dependence is driven by individual access to resources. Other circumstances may require different formulations, but modelers must ensure that these have appropriate scaling and non-equilibrium behavior.     

Relationship between a high density of sika deer and productivity of the short-grass (<Emphasis Type="Italic">Zoysia japonica</Emphasis>) community: a case study on Kinkazan Island,northern Japan

An extremely high-density (ca. 800 deer km^–2) wild sika deer population uses a short-grass community dominated by Zoysia japonica on Kinkazan Island in northeastern Japan. To explain why the density of wild deer is quite high on the Zoysia community, (1) we quantified the seasonal productivity of the Zoysia community, (2) we compared food availabilities among the plant communities, and (3) we described the habitat selection by the deer in different seasons. Food availability was greater on the Zoysia community than in the forest understory from spring to fall. The productivity of the Zoysia community was high enough to support the actual high density of the deer (814 deer km^–2) in summer. However, the productivity markedly decreased in winter, when the deer density decreased to less than half (358 deer km^–2) of the summer value. In contrast, the deer density of the adjacent forests was highest in winter (154 deer km^–2) and lowest in spring (19 deer km^–2). These results suggest that the deer using the Zoysia community in summer left and were absorbed into the adjacent forest in winter. If such an adjacent community were absent, many deer would not survive, and consequently the deer density on the Zoysia community in summer would not be so high. This intercommunity movement is particularly important for the deer using a plant community like the Zoysia community, which is highly productive but has a small standing biomass.     

The neglected tool in the Bayesian ecologist's shed: a case study testing informative priors' effect on model accuracy

Despite benefits for precision, ecologists rarely use informative priors. One reason that ecologists may prefer vague priors is the perception that informative priors reduce accuracy. To date, no ecological study has empirically evaluated data‐derived informative priors' effects on precision and accuracy. To determine the impacts of priors, we evaluated mortality models for tree species using data from a forest dynamics plot in Thailand. Half the models used vague priors, and the remaining half had informative priors. We found precision was greater when using informative priors, but effects on accuracy were more variable. In some cases, prior information improved accuracy, while in others, it was reduced. On average, models with informative priors were no more or less accurate than models without. Our analyses provide a detailed case study on the simultaneous effect of prior information on precision and accuracy and demonstrate that when priors are specified appropriately, they lead to greater precision without systematically reducing model accuracy.     

The impact of demographic changes on the epidemiology of herpes zoster: Spain as a case study

Varicella zoster virus (VZV) causes varicella upon first exposure and may reactivate later in life into herpes zoster (HZ), with a risk that is thought to be reduced by re-exposures to VZV. Given the decades-long time scales of reactivation and its dependence on the accumulation of re-exposure episodes, adopting a long-term perspective may be useful to correctly interpret current epidemiological trends of VZV. In this study, we investigate the possible impact of demographic changes on varicella and HZ in Spain, using an age-structured mathematical model informed with historical demographic data and calibrated against age-specific profiles of varicella seroprevalence and HZ incidence data. The model qualitatively reproduces the remarkable growth of HZ incidence observed in Spain between 1997 and 2004, before the introduction of varicella vaccination programmes. We demonstrate that this growth may be partially ascribed to the reduction of varicella circulation that followed the overall decline of the birth rate in the twentieth century. Model predictions further suggest that, even under the most optimistic projections, HZ incidence will continue its rise until at least 2040. Considering the effect of demographic changes can help interpreting variations in epidemiological trends of HZ, contributing to a more accurate evaluation of vaccination programmes against VZV.     

An in-host model of acute infection: measles as a case study

The epidemiology of acute infections is strongly influenced by the immune status of individuals. In-host models can provide quantitative predictions of immune status and can thus offer valuable insights into the factors that influence transmission between individuals and the effectiveness of vaccination protocols with respect to individual immunity. Here we develop an in-host model of measles infection. The model explicitly considers the effects of immune system memory and CD8 T-cells, which are key to measles clearance. The model is used to determine the effects of waning immunity through vaccination and infection, the effects of booster exposures or vaccines on the level of immunity, and the immune system characteristics that result in measles transmission (R(0)>1) even if an individual has no apparent clinical symptoms. We find that the level of immune system CD8 T-cells at the time of exposure to measles determines whether an individual will experience a measles infection or simply a boost in immunity. We also find that the infected cell dynamics are a good indicator of measles transmission and the degree of symptoms that will be experienced. Our results indicate that the degree of immunity in adults is independent of the source of exposure in early childhood, be it vaccine or natural infection.     

Understanding basic species population dynamics for effective control: a case study on community-led culling of the common myna (Acridotheres tristis)

Population manipulation of introduced species can be difficult and many widespread eradication or reduction attempts have failed. Understanding the population dynamics of a species is essential for undertaking a successful control program. Despite this, control attempts are frequently undertaken with limited knowledge of the species population dynamics. For example, in Australia, concern over the impact of the introduced common myna (Acridotheres tristis) has led to community members culling the species. In this paper, we assessed the impact of community-led common myna culling program over broad and fine-scales in Canberra, Australia. We utilized a basic population model to enhance understanding of common myna population dynamics and the potential influence of various culling regimes. We found a significant negative relationship between common myna abundance and culling at fine-scales (1 km²). However, over broad-scales the relationship between common myna abundance and culling was not significant. Our population model indicated culling at a rate of 25 birds per km² per year would reduce common myna abundance, regardless of initial density. Our results suggest that currently too few individuals are being removed from the Canberra population, and natural reproduction, survival and/or immigration is able to replace the culled individuals. This highlights the value of undertaking basic population modeling to assess if potential control measures are capable of achieving desired outcomes. Our work provides information for researchers, government and community groups interested in controlling not only the common myna, but also other introduced species.